| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/iuc/circexplorer2/circexplorer2/2.3.8+galaxy0 (this tool) |
| circexplorer2 |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| circexplorer2 | 2.3.8 | package |
| Additional information about this tool |
#if $mode.selector == 'align'
mkdir -p reads &&
#set file_paths = []
#for $i,$input_file in enumerate($mode.fastq)
#set $fname = 'file' + str($i) + "." + $input_file.ext
#set $file_path = 'reads/' + $fname
ln -s '$input_file' '$file_path' &&
$file_paths.append($file_path)
#end for
CIRCexplorer2 align
--thread=\${GALAXY_SLOTS:-10}
--gtf '$mode.gtf'
-g '$mode.genome'
--fastq #echo ','.join($file_paths)#
$mode.bw
$mode.scale
$mode.skip_tophat
$mode.skip_tophat_fusion
&& tar -zcvf alignment.tgz './alignment'
#else if $mode.selector == 'parse'
CIRCexplorer2 parse
-t $mode.aligner.selector
$mode.aligner.fusion_file
#if $mode.aligner.selector == 'TopHat-Fusion'
$mode.aligner.pe
#end if
$mode.aligner.f
#else if $mode.selector == 'annotate'
ln -s $mode.genome reference_genome.fa &&
CIRCexplorer2 annotate
-r $mode.ref
-g reference_genome.fa
-b $mode.bed
$mode.no_fix
$mode.low_confidence
#else if $mode.selector == 'assemble'
tar -zxf $mode.tophat &&
CIRCexplorer2 assemble
--thread=\${GALAXY_SLOTS:-10}
-r $mode.ref
-m ./alignment
$mode.remove_rRNA
&& tar -zcvf assemble.tgz './assemble'
#else
ln -s '$mode.genome' reference_genome.fa &&
#if $mode.assemble_file.ext.endswith(".gz")
tar -zxf $mode.assemble_file &&
#else
tar -xf $mode.assemble_file &&
#end if
#if $mode.as_option.selector == 'enabled'
tar -zxf $mode.as_option.tophat &&
#end if
CIRCexplorer2 denovo
-d ./assemble
-r $mode.ref
-b $mode.bed
-g reference_genome.fa
#if $mode.abs
--abs 'abs'
#end if
#if $mode.as_option.selector == 'enabled'
--as 'as'
$mode.as_option.type_mapping './alignment'
#end if
$mode.no_fix
$mode.rpkm
#end if
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
mode|gtf: annotation_01.gtf mode|genome: reference_01.fa mode|fastq: ['reads_01.fastq', 'reads_02.fastq', 'reads_03.fastq'] mode|skip_tophat_fusion: True mode|selector: align |
name: value |
annotation_01.gtf reference_01.fa reads_01.fastq reads_02.fastq reads_03.fastq value |
| Test-2 |
mode|gtf: annotation_01.gtf mode|genome: reference_01.fa mode|fastq: ['reads_01.fastq.gz', 'reads_02.fastq.gz', 'reads_03.fastq.gz'] mode|bw: True mode|scale: True mode|skip_tophat_fusion: True mode|selector: align |
name: value name: value |
annotation_01.gtf reference_01.fa reads_01.fastq.gz reads_02.fastq.gz reads_03.fastq.gz value |
| Test-3 |
mode|aligner|fusion_file: mapsplice_chimeric.junction mode|aligner|selector: MapSplice mode|selector: parse |
name: value |
mapsplice_chimeric.junction value |
| Test-4 |
mode|aligner|fusion_file: STAR_chimeric.junction mode|aligner|f: True mode|aligner|selector: STAR mode|selector: parse |
name: value |
STAR_chimeric.junction value |
| Test-5 |
mode|ref: annotation_02.txt mode|genome: reference_02.fa mode|bed: test_04.bed mode|selector: annotate |
name: value |
annotation_02.txt reference_02.fa test_04.bed value |
| Test-6 |
mode|ref: annotation_02.txt mode|genome: reference_02.fa mode|bed: test_04.bed mode|no_fix: True mode|low_confidence: True mode|selector: annotate |
name: value |
annotation_02.txt reference_02.fa test_04.bed value |
| Test-7 |
mode|ref: annotation_02.txt mode|bed: test_04.bed mode|genome: reference_02.fa mode|assemble_file: assemble.tgz mode|selector: denovo |
name: value name: value name: value name: value |
annotation_02.txt test_04.bed reference_02.fa assemble.tgz value |
| Test-8 |
mode|ref: annotation_02.txt mode|bed: test_04.bed mode|genome: reference_02.fa mode|assemble_file: assemble.tgz mode|abs: True mode|no_fix: True mode|rpkm: True mode|selector: denovo |
name: value name: value name: value name: value name: value name: value |
annotation_02.txt test_04.bed reference_02.fa assemble.tgz value |